The game is set up with a "duration" count on the inhabitants of Black City/White Forest. After all inhabiants have left all the buildings/bushes also disappear to reflect the lack of population. You need to "re-populate" the area. Currently, this "could" be done with an Action Replay HOWEVER the people that have the know how have not shared this for the Action Replay. There are various programs out there (such as BW PokeStock) which include tools for re-populating the Black City/White Forest HOWEVER these require you to be able to back up your game's save file which is something most people cannot do (unless using illegal roms.)
The only way the game "naturally" repairs an "empty" Black City/White Forest is when the Entralink is activated.